I would take it one step further:
An MSc is more theoretical, where an MBA is more practical. If your goal is more school (a PhD or a post-doc), then by all means an MSc is good for you. If you want to go to school for two years and hit the ground working, then do an MBA.
Additionally, since it is a more practice-oriented degree, most MBA programs require you to have two years or more of work experience, whereas MScs are less stringent in this area.
There are a lot of good MBA programs in Canada: McGill, Concordia, York, Ivey. Read more on this article on this site:
http://www.find-mba.com/article/391/mba-programs-in-canada-maple-trees-bacon-and-business-schools